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The University Museum at the University of Tokyo
Fluid Analysis Uncovers the Biophysiological Nature of Ancient Organisms

Instead of traditional qualitative research methods, a project assistant professor Yuta Shiino (Ph.D.) from the University Museum at the University of Tokyo applied computatinal fluid dynamics (CFD) simulation. By performing fluid analyses of fossil brachiopods and trilobites, he succeeded in exposing the biology of the ancient organisms, which was not easily identified using traditional research methods.

Picture 1: Yuta Shiino (Ph.D.),
Project Assistant Professor,
Museum Group for Promoting Cutting-Edge,
Research in Macroscopic Sciences,
the University Museum, the University Tokyo

 Paleontology is often associated with researchers hunting for fossils in woods and mountains, and looking for new species to add to the classification chart. A few exceptions exist among paleontologists. Dr. Shiino, who works for the Museum Group for Promoting Cutting-Edge Research in Macroscopic Sciences, pursues research from a different approach. Dr. Shiino describes this research as “a study to uncover the living motions from unmoving fossils.” Dr. Shiino started using SC/Tetra to perform fluid analyses during his doctoral program where he used CFD simulation to understand the lives of ancient underwater organisms.

Fluid Analysis of Brachiopods: A Species that Prospered in the Paleozoic Era

 Dr. Shiino first started using fluid analysis to study brachiopods. The brachiopods were at their peak in the Paleozoic Era spanning 250 to 540 million years ago, and they have marginally survived in the ocean today. Despite an appearance that resembles bivalves, brachiopods are completely different organisms. Bivalves, which include clams, oysters, and mussels, contain a muscular body inside their shell. In contrast, brachiopods consist of virtually hollow shells. Brachiopod tentacles align alongside thin bones for filtering food and providing respiration. Bivalves permit water to flow in and out through siphons for food filtration and respiration. Brachiopods are inferior to circulate water on their own, nor actively move, as they cleverly use the water that naturally flows inside the shell through small gape to perform their life functions. This underlines how important effective water distribution is for their food filtration and respiration. “They are the ultimate couch potatoes, so to speak,” explains Dr. Shiino with a smile. He used CFD to simulate how brachiopods use water flow to support their natural biological functions.

Figure 1: A model and fossil of a brachiopod (spiral thin bones are reproduced by aluminum wires for water flow tests)

Limitation of Experiments

 Dr. Shiino’s first research target was the spirifer, also known as the Swallow Stone in China, a type of brachiopods, which can have diverse body shapes. Because of its unique characteristic of having spiral food-filtering organ carpal bones (shown in Figure 1), many researchers have conducted experiments to investigate the relationship between the brachiopod body shapes and fluid flow. However, difficulties in visualizing the fluid flow during the tests limited the research to more of the qualitative level. As a result, an endless cycle of new theories and counter theories continued until recently. Having conducted his own water flow experiments, Dr. Shiino believed that more quantitative results were in demand. He considered using high-end experimental equipment that would generate more accurate data, but the cost and construction time to improve the equipment was unrealistic. That helped him with making a firm decision to apply fluid analysis.

Figure 2: Paraspirifer fossil (on left) and
model diagram (on right)
Click to enlarge.

Figure 3: Flow simulation around the model with streamlines (flows for ventral valve in above,
​for dorsal valve below).
Click to enlarge.

Fluid Analysis Encouraged an Alternative Interpretation​

 The median depression of a brachiopod, which resembles a beak, is called the sulcus. The convex side of the shell is called the dorsal valve, while the concave side anterior (Figure 2). Dr. Shiino used fluid analyses to evaluate the effects of water flowing from both dorsal and ventral valves (Figure 3). Although the detected flow rate was small, the result showed that the water always entered from the central sulcus and exited from the gapes lateral to the sulcus regardless of the flow directions and velocity. Dr. Shiino also found that the water coming from the sulcus circulated along the spiral bones toward each end.

  Two theories were dominant prior to Dr. Shiino’s finding: one suggested that water entered from both ends and exited from the sulcus. Another hypothesized that water entered from sulcus and exited from both ends. No one suspected of the spiral swirling water flowing through the shell. Dr. Shiino has repeated analyses with different configurations, but the result was consistent throughout. Water enters from the center and leaves from the remain due to the constant pressure difference along the gape. Effective food filtration and respiration were made possible by the spiral swirling water flow created inside the shell, which increased the tentacle surface along the spiral bone with respect to incoming water.

 The spiral swirling water flow and the locations of inlet/outlet were also confirmed in a precise experiment using detailed model. Dr. Shiino says that he received sharp criticisms when he first presented the results in a paper, but scientists now agree, to some extent, that the mechanism Dr. Shiino proposes is biologically reasonable. In addition, the quantitative and qualitative approaches to research from several other brachiopods have shown similar results.

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*Contents and specifications of products are as of February 1, 2014 and subject to change without notice. We shall not be held liable for any errors in figures and pictures, or any typographical errors.

Institute Details


The University Museum at the University of Tokyo
Established April 1966
Administrative Body The University of Tokyo
Location Hongo, Bunkyo-ku, Tokyo, Japan


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